+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outline_actionPerformed();\r
+ }\r
+ });\r
+ nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideMenuItem_actionPerformed();\r
+ }\r
+ });\r
+ colourMenu.setText("Group Colour");\r
+ showBoxes.setText("Boxes");\r
+ showBoxes.setState(true);\r
+ showBoxes.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showBoxes_actionPerformed();\r
+ }\r
+ });\r
+ showText.setText("Text");\r
+ showText.setState(true);\r
+ showText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showText_actionPerformed();\r
+ }\r
+ });\r
+ showColourText.setText("Colour Text");\r
+ showColourText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showColourText_actionPerformed();\r
+ }\r
+ });\r
+ editMenu.setText("Edit");\r
+ cut.setText("Cut");\r
+ cut.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ });\r
+ upperCase.setText("To Upper Case");\r
+ upperCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ });\r
+ lowerCase.setText("To Lower Case");\r
+ lowerCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ toggle.setText("Toggle Case");\r
+ toggle.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ pdbMenu.setText("Associate Structure with Sequence");\r
+ pdbFromFile.setText("From File");\r
+ pdbFromFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pdbFromFile_actionPerformed();\r
+ }\r
+ });\r
+ enterPDB.setText("Enter PDB Id");\r
+ enterPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ enterPDB_actionPerformed();\r
+ }\r
+ });\r
+ discoverPDB.setText("Discover PDB ids");\r
+ discoverPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ discoverPDB_actionPerformed();\r
+ }\r
+ });\r
+ outputMenu.setText("Output to Textbox...");\r
+ sequenceFeature.setText("Create Sequence Feature");\r
+ sequenceFeature.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceFeature_actionPerformed();\r
+ }\r
+ });\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed();\r
+ }\r
+ });\r
+ jMenu1.setText("Group");\r
+ add(groupMenu);\r
+\r
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(jMenu1);\r
+ sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(textColour);\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ colourMenu.add(userDefinedColour);\r
+\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r